HEADER ELECTRON TRANSPORT 28-JUN-04 1WLI TITLE L122Y MUTANT OF FMN-BINDING PROTEIN FROM DESULFOVIBRIO VULGARIS TITLE 2 (MIYAZAKI F) COMPND MOL_ID: 1; COMPND 2 MOLECULE: FMN-BINDING PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DESULFOVIBRIO VULGARIS STR. 'MIYAZAKI F'; SOURCE 3 ORGANISM_TAXID: 883; SOURCE 4 STRAIN: MIYAZAKI F; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ELECTRON TRANSPORT, FLAVOPROTEIN, FMN EXPDTA X-RAY DIFFRACTION AUTHOR N.SHIBATA,Y.HIGUCHI REVDAT 5 25-OCT-23 1WLI 1 REMARK REVDAT 4 10-NOV-21 1WLI 1 REMARK SEQADV REVDAT 3 28-APR-09 1WLI 1 JRNL REVDAT 2 24-FEB-09 1WLI 1 VERSN REVDAT 1 19-JUL-05 1WLI 0 JRNL AUTH M.KITAMURA,K.TERAKAWA,H.INOUE,T.HAYASHIDA,K.SUTO,Y.MORIMOTO, JRNL AUTH 2 N.YASUOKA,N.SHIBATA,Y.HIGUCHI JRNL TITL DETERMINATION OF THE ROLE OF THE CARBOXYL-TERMINAL JRNL TITL 2 LEUCINE-122 IN FMN-BINDING PROTEIN BY MUTATIONAL AND JRNL TITL 3 STRUCTURAL ANALYSIS. JRNL REF J.BIOCHEM. V. 141 459 2007 JRNL REFN ISSN 0021-924X JRNL PMID 17261542 JRNL DOI 10.1093/JB/MVM051 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.153 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.153 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1414 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 27871 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.152 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1446 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 27436 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1860 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 62 REMARK 3 SOLVENT ATOMS : 255 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 2177.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 5 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 8895 REMARK 3 NUMBER OF RESTRAINTS : 8133 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 ANGLE DISTANCES (A) : 0.023 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.027 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.045 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.057 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.020 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.054 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1WLI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-JUN-04. REMARK 100 THE DEPOSITION ID IS D_1000023708. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : OXFORD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29692 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO REMARK 200 SOFTWARE USED: SHELXL-97 REMARK 200 STARTING MODEL: 1FLM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG6000, SODIUM ACETATE, TRIS, PH 7.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 39.69550 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 63 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 ASP B 61 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG B 71 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 ARG B 86 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG B 86 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 ASP B 94 CB - CG - OD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP B 24 56.23 -147.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN A 1123 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN B 2123 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FLM RELATED DB: PDB REMARK 900 RELATED ID: 1WLK RELATED DB: PDB REMARK 900 L122E MUTANT REMARK 900 RELATED ID: 1WLL RELATED DB: PDB REMARK 900 L122K MUTANT DBREF 1WLI A 1 122 UNP Q46604 FMNB_DESVM 1 122 DBREF 1WLI B 1 122 UNP Q46604 FMNB_DESVM 1 122 SEQADV 1WLI TYR A 122 UNP Q46604 LEU 122 ENGINEERED MUTATION SEQADV 1WLI TYR B 122 UNP Q46604 LEU 122 ENGINEERED MUTATION SEQRES 1 A 122 MET LEU PRO GLY THR PHE PHE GLU VAL LEU LYS ASN GLU SEQRES 2 A 122 GLY VAL VAL ALA ILE ALA THR GLN GLY GLU ASP GLY PRO SEQRES 3 A 122 HIS LEU VAL ASN THR TRP ASN SER TYR LEU LYS VAL LEU SEQRES 4 A 122 ASP GLY ASN ARG ILE VAL VAL PRO VAL GLY GLY MET HIS SEQRES 5 A 122 LYS THR GLU ALA ASN VAL ALA ARG ASP GLU ARG VAL LEU SEQRES 6 A 122 MET THR LEU GLY SER ARG LYS VAL ALA GLY ARG ASN GLY SEQRES 7 A 122 PRO GLY THR GLY PHE LEU ILE ARG GLY SER ALA ALA PHE SEQRES 8 A 122 ARG THR ASP GLY PRO GLU PHE GLU ALA ILE ALA ARG PHE SEQRES 9 A 122 LYS TRP ALA ARG ALA ALA LEU VAL ILE THR VAL VAL SER SEQRES 10 A 122 ALA GLU GLN THR TYR SEQRES 1 B 122 MET LEU PRO GLY THR PHE PHE GLU VAL LEU LYS ASN GLU SEQRES 2 B 122 GLY VAL VAL ALA ILE ALA THR GLN GLY GLU ASP GLY PRO SEQRES 3 B 122 HIS LEU VAL ASN THR TRP ASN SER TYR LEU LYS VAL LEU SEQRES 4 B 122 ASP GLY ASN ARG ILE VAL VAL PRO VAL GLY GLY MET HIS SEQRES 5 B 122 LYS THR GLU ALA ASN VAL ALA ARG ASP GLU ARG VAL LEU SEQRES 6 B 122 MET THR LEU GLY SER ARG LYS VAL ALA GLY ARG ASN GLY SEQRES 7 B 122 PRO GLY THR GLY PHE LEU ILE ARG GLY SER ALA ALA PHE SEQRES 8 B 122 ARG THR ASP GLY PRO GLU PHE GLU ALA ILE ALA ARG PHE SEQRES 9 B 122 LYS TRP ALA ARG ALA ALA LEU VAL ILE THR VAL VAL SER SEQRES 10 B 122 ALA GLU GLN THR TYR HET FMN A1123 31 HET FMN B2123 31 HETNAM FMN FLAVIN MONONUCLEOTIDE HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 3 FMN 2(C17 H21 N4 O9 P) FORMUL 5 HOH *255(H2 O) HELIX 1 1 PRO A 3 LYS A 11 1 9 HELIX 2 2 SER A 34 LEU A 36 5 3 HELIX 3 3 MET A 51 ASP A 61 1 11 HELIX 4 4 ASP A 94 ALA A 100 1 7 HELIX 5 5 PRO B 3 LEU B 10 1 8 HELIX 6 6 SER B 34 LEU B 36 5 3 HELIX 7 7 MET B 51 ASP B 61 1 11 HELIX 8 8 ASP B 94 ALA B 100 1 7 SHEET 1 A 7 GLY A 25 TRP A 32 0 SHEET 2 A 7 VAL A 15 GLY A 22 -1 N ILE A 18 O VAL A 29 SHEET 3 A 7 ARG A 63 SER A 70 -1 O LEU A 65 N ALA A 19 SHEET 4 A 7 THR A 81 ARG A 92 -1 O ILE A 85 N MET A 66 SHEET 5 A 7 ALA A 109 TYR A 122 -1 O GLU A 119 N LEU A 84 SHEET 6 A 7 ARG A 43 VAL A 48 -1 N ILE A 44 O ILE A 113 SHEET 7 A 7 LYS A 37 LEU A 39 -1 N LEU A 39 O ARG A 43 SHEET 1 B 7 PRO B 26 TRP B 32 0 SHEET 2 B 7 VAL B 15 GLN B 21 -1 N ILE B 18 O VAL B 29 SHEET 3 B 7 ARG B 63 SER B 70 -1 O LEU B 65 N ALA B 19 SHEET 4 B 7 THR B 81 ARG B 92 -1 O ILE B 85 N MET B 66 SHEET 5 B 7 ALA B 109 GLN B 120 -1 O VAL B 116 N ARG B 86 SHEET 6 B 7 ARG B 43 VAL B 48 -1 N ILE B 44 O ILE B 113 SHEET 7 B 7 LYS B 37 LEU B 39 -1 N LYS B 37 O VAL B 45 SITE 1 AC1 20 HIS A 27 VAL A 29 ASN A 30 THR A 31 SITE 2 AC1 20 TRP A 32 TYR A 35 PRO A 47 GLY A 49 SITE 3 AC1 20 GLY A 50 MET A 51 HIS A 52 LYS A 53 SITE 4 AC1 20 THR A 54 TRP A 106 HOH A1127 HOH A1223 SITE 5 AC1 20 GLY B 82 THR B 121 TYR B 122 HOH B2162 SITE 1 AC2 21 GLY A 82 THR A 121 TYR A 122 HOH A1125 SITE 2 AC2 21 HOH A1169 HIS B 27 VAL B 29 ASN B 30 SITE 3 AC2 21 THR B 31 TRP B 32 TYR B 35 PRO B 47 SITE 4 AC2 21 GLY B 49 GLY B 50 MET B 51 HIS B 52 SITE 5 AC2 21 LYS B 53 THR B 54 HOH B2124 HOH B2204 SITE 6 AC2 21 HOH B2209 CRYST1 36.673 79.391 39.970 90.00 91.25 90.00 P 1 21 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.027268 0.000000 0.000595 0.00000 SCALE2 0.000000 0.012596 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025025 0.00000